All clone tables

All datasets’ clone information tables, in each table we show the clone CTaa, the status (shared clone or unique clone), the number of occurence in each sample, the total number of occurence, and the Shannon entropy.

Saved file name: All_clone_tables/All_clones_in_dataset name.xlsx

Dataset: Dataset1_GFP

Dataset: Dataset1_CD45

Dataset: Dataset2

Dataset: Dataset3

Dataset: Dataset4_m366_vs_m367

Dataset: Dataset4_m366_vs_m368

Dataset: Dataset4_m366_vs_m369

Dataset: Dataset4_m367_vs_m368

Dataset: Dataset4_m367_vs_m369

Dataset: Dataset4_m368_vs_m369

Merged Shannon entropy tables (all real clone and sampled cells)

These data tables are used to compare the Shannon entropy of real clones and sampled cells

Tables

Saved file name: Merged_real_clone_and_sampled_cells_Shannon_entropy/merge_all_sampled_and_real_Shannon_entropy_dataset name.xlsx

Dataset: Dataset1_GFP

Dataset: Dataset1_CD45

Dataset: Dataset2

Dataset: Dataset3

Dataset: Dataset4_m366_vs_m367

Dataset: Dataset4_m366_vs_m368

Dataset: Dataset4_m366_vs_m369

Dataset: Dataset4_m367_vs_m368

Dataset: Dataset4_m367_vs_m369

Dataset: Dataset4_m368_vs_m369

Boxplot

Dataset Dataset1_GFP

Dataset Dataset1_CD45

Dataset Dataset2

Dataset Dataset3

Dataset Dataset4_m366_vs_m367

Dataset Dataset4_m366_vs_m368

Dataset Dataset4_m366_vs_m369

Dataset Dataset4_m367_vs_m368

Dataset Dataset4_m367_vs_m369

Dataset Dataset4_m368_vs_m369

Double y-axis plots (Number of clones (real clone - sampled cells) and Shannon entropy), all

Saved file name: Input_for_double_y_axis_plots/summmary_real_clone_and_sampled_clones_Shannon_entropy_dataset_dataset name.xlsx

Tables

Dataset Dataset1_GFP

Dataset Dataset1_CD45

Dataset Dataset2

Dataset Dataset3

Dataset Dataset4_m366_vs_m367

Dataset Dataset4_m366_vs_m368

Dataset Dataset4_m366_vs_m369

Dataset Dataset4_m367_vs_m368

Dataset Dataset4_m367_vs_m369

Dataset Dataset4_m368_vs_m369

Figures

Dataset Dataset1_GFP

### Dataset Dataset1_CD45

### Dataset Dataset2

### Dataset Dataset3

### Dataset Dataset4_m366_vs_m367

### Dataset Dataset4_m366_vs_m368

### Dataset Dataset4_m366_vs_m369

### Dataset Dataset4_m367_vs_m368

### Dataset Dataset4_m367_vs_m369

### Dataset Dataset4_m368_vs_m369

Double y-axis plots (Number of clones (real clone - sampled cells) and Shannon entropy), >= 10 cells only

Saved file name: Input_for_double_y_axis_plots_filter10cells/summmary_real_clone_and_sampled_clones_Shannon_entropy_dataset_dataset name.filter10cells.xlsx

Tables

Dataset Dataset1_GFP

Dataset Dataset1_CD45

Dataset Dataset2

Dataset Dataset3

Dataset Dataset4_m366_vs_m367

Dataset Dataset4_m366_vs_m368

Dataset Dataset4_m366_vs_m369

Dataset Dataset4_m367_vs_m368

Dataset Dataset4_m367_vs_m369

Dataset Dataset4_m368_vs_m369

Figures

Dataset Dataset1_GFP

### Dataset Dataset1_CD45

### Dataset Dataset2

### Dataset Dataset3

### Dataset Dataset4_m366_vs_m367

### Dataset Dataset4_m366_vs_m368

### Dataset Dataset4_m366_vs_m369

### Dataset Dataset4_m367_vs_m368

### Dataset Dataset4_m367_vs_m369

### Dataset Dataset4_m368_vs_m369

MHI

Note

In the Dataset 4, the following comparisons do not have any “shared clones” between the 2 samples:

  • m366 vs m368

  • m366 vs m369

  • m367 vs m368

  • m367 vs m369

we exclude these comparisons from the analysis of Dataset 4.

MHI + Shannon entropy tables

Tables which contain the clone information, Shannon entropy and MHI of shared clones between samples. Empty cells (NA cells) mean that the clone is not shared in the samples or the number of occurrences less than 10.

Save file names: Dataset1_CD45.xlsx, Dataset1_GFP.xlsx, Dataset2.xlsx, Dataset4_m366_vs_m367.xlsx, Dataset3.xlsx, Dataset4_m368_vs_m369.xlsx

Dataset Dataset1_GFP

Dataset Dataset1_CD45

Dataset Dataset2

Dataset Dataset3

Dataset Dataset4_m366_vs_m367

Dataset Dataset4_m368_vs_m369

MHI of clone vs. clone

Tables which contain the MHI of clone versus clone, where clones are selected from different categories: “unique clones”, “shared in 3 samples clones” or “shared in 2 samples clones”. Available comparisons are: “shared clones” vs “shared clones”, “unique clones” vs “unique clones”, “shared clones” vs “unique clones”. Clones are required to have more than 10 cells in every sample in the dataset, not total >= 10 cells.

In this analysis we just consider Dataset 2, Dataset 3 and Dataset 4.

Since tables in this section are too large, we do not display them in HTML file. Please find the saved .xlsx file in the One Drive folder.

Dataset 2

Group shared vs shared

[1] “Table saved as MHI_clone_vs_clone/MHI_shared vs shared_Dataset2.xlsx” #### Group unique vs shared

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs shared_Dataset2.xlsx” #### Group unique vs unique

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs unique_Dataset2.xlsx”

Dataset 3

[1] “Table saved as MHI_clone_vs_clone/MHI_shared vs shared_Dataset3.xlsx”

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs shared_Dataset3.xlsx”

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs unique_Dataset3.xlsx”

Dataset 4 m366 vs m367

Group shared vs shared

[1] “Table saved as MHI_clone_vs_clone/MHI_shared vs shared_Dataset4_m366_vs_m367.xlsx” #### Group unique vs shared

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs shared_Dataset4_m366_vs_m367.xlsx” #### Group unique vs unique

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs unique_Dataset4_m366_vs_m367.xlsx”

Dataset 4 m368 vs m369

Group shared vs shared

[1] “Table saved as MHI_clone_vs_clone/MHI_shared vs shared_Dataset4_m368_vs_m369.xlsx” #### Group unique vs shared

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs shared_Dataset4_m368_vs_m369.xlsx” #### Group unique vs unique

[1] “Table saved as MHI_clone_vs_clone/MHI_unique vs unique_Dataset4_m368_vs_m369.xlsx”

Combine MHI “same clone, sample vs sample” and “clone vs clone”

Tables

Since tables in this section are too large, we do not display them in HTML file. Please find the saved .xlsx file in the One Drive folder.

Save file names: combine_MHI_sample_vs_sample_and_clone_vs_clone_dataset name.xlsx

Dataset Dataset2

[1] “Table saved as Combined_MHI/combine_MHI_sample_vs_sample_and_clone_vs_clone_Dataset2.xlsx” #### Dataset Dataset3

[1] “Table saved as Combined_MHI/combine_MHI_sample_vs_sample_and_clone_vs_clone_Dataset3.xlsx” #### Dataset Dataset4_m366_vs_m367

[1] “Table saved as Combined_MHI/combine_MHI_sample_vs_sample_and_clone_vs_clone_Dataset4_m366_vs_m367.xlsx” #### Dataset Dataset4_m368_vs_m369

[1] “Table saved as Combined_MHI/combine_MHI_sample_vs_sample_and_clone_vs_clone_Dataset4_m368_vs_m369.xlsx”

Figures

Dataset Dataset2

Dataset Dataset3

Dataset Dataset4_m366_vs_m367

Dataset Dataset4_m368_vs_m369

Final QC metrics after filtering out low-QC cells

Dataset1

Dataset2

Dataset3

Dataset4